annotSite | Annotate modification site |
dataProcessPlotsPTM | Visualization for explanatory data analysis |
dataSummarizationPTM | Process MS PTM and global protein data |
dataSummarizationPTM_TMT | Process MS PTM and global protein data produced via tandem mass tag labeling |
designSampleSizePTM | Planning future experimental designs of PTM experiments in sample size calculation |
groupComparisonPlotsPTM | Visualization for model-based analysis and summarization |
groupComparisonPTM | Model PTM and/or protein data and make adjustments if needed |
locateMod | Locate modified sites with a peptide |
locatePTM | Annotate modified sites with associated peptides |
MaxQtoMSstatsPTMFormat | Convert output of TMT labeled MaxQuant experiment into MSstatsPTM format |
MSstatsPTM | MSstatsPTM: A package for detecting differencially abundant post translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic experiments. |
MSstatsPTMSiteLocator | Locate modification site number and amino acid |
PDtoMSstatsPTMFormat | Convert Proteome Discoverer output into MSstatsPTM format |
PhilosophertoMSstatsPTMFormat | Convert output of TMT labaled Fragpipe (Philosopher) data into MSstatsPTM format. |
ProgenesistoMSstatsPTMFormat | Converts non-TMT Progenesis output into the format needed for MSstatsPTM |
PStoMSstatsPTMFormat | Convert Peaks Studio output into MSstatsPTM format |
raw.input | Example of input PTM dataset for LabelFree/DDA/DIA experiments. |
raw.input.tmt | Example of input PTM dataset for TMT experiments. |
SkylinetoMSstatsPTMFormat | Convert Skyline output into MSstatsPTM format |
SpectronauttoMSstatsPTMFormat | Convert Spectronaut output into MSstatsPTM format |
summary.data | Example of output from dataSummarizationPTM function for non-TMT data |
summary.data.tmt | Example of output from dataSummarizationPTM_TMT function for TMT data |
tidyFasta | Read and tidy a FASTA file |